If you're using a slightly older libX11 that doesn't have the x11-xcb stuff built in, you can't configure startup-notification.
The tail of the output when building on NetBSD 5.0 using the pkgsrc buid framework:
checking whether realloc (NULL,) will work... yes
checking execinfo.h usability... no
checking execinfo.h presence... no
checking for execinfo.h... no
checking pkg-config is at least version 0.9.0... yes
checking for xcb... yes
checking for xcb_aux... yes
checking for xcb_event... yes
checking for x11_xcb... no
configure: error: Cannot find x11-xcb
*** Error code 1
Stop.
make: stopped in /usr/pkgsrc/x11/startup-notification
*** Error code 1
Stop.
This breaks (for me) devel/monotone-viz (via x11/lablgtk, x11/gnome-panel,
and devel/libwnck), and some more packages.
Some option to build without this bleeding-edge support "would be nice".
I also reported this to the pkgsrc people; maybe they can find some workaround, but a real fix is of course better. See http://mail-index.netbsd.org/pkgsrc-users/2011/10/08/msg015143.html for any possible followup on that front (none so far).